v1.28.0

v1.28.0 (2024-12-18)

Features

• Add io/readers to ruff config (#94, 7efc97b)

Updated include list to have the io/readers functions and updated the files so all ruff tests pass.

## Summary by CodeRabbit

• New Features

• Enhanced flexibility in loading feature files by accepting both Path objects and strings.

• Improved error handling and logging for file loading and directory access.

• Bug Fixes

• Enhanced error handling and logging for file loading and directory access, providing clearer context for issues.

• Documentation

• Updated docstrings for functions to improve clarity and detail, including return type annotations.

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Detailed Changes: v1.27.0...v1.28.0

v1.27.0

v1.27.0 (2024-12-17)

Features

• Add analysis functions (#92, a57182c)

Includes correlation calculations and plotting those correlations as a heatmap and histogram

• New Features - Updated version number to 1.26.0 with new dependencies: numpy, seaborn, and pandas. - Introduced a new module for analyzing READII outputs with several correlation functions. - Added visualization functions for correlation data: heatmap and histogram. - New validation function for DataFrame dimensions added. - Expanded platform support to include osx-64 and win-64.

• Bug Fixes - Enhanced error handling in correlation calculations and plot saving processes. - Simplified exception handling in feature loading functions.

• Documentation - Improved docstrings for new functions and modules for better usability.

• Chores - Expanded linting configuration for broader coverage of Python files.

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Detailed Changes: v1.26.0...v1.27.0

v1.26.0

v1.26.0 (2024-12-16)

Features

• Expand platform support in pixi and CI/CD workflow (#91, 546fe5c)

This PR adds the windows platform and older mac platform to the pixi configuration so developers with those machines can be assured that they can contribute to this project without running into dependency issues

• also add a testing branch to test with windows across all configured python versions

Summary by CodeRabbit

• New Features

  • Expanded testing environment to include Windows support.
  • Updated project version to "1.25.0".
  • Added support for additional platforms: "osx-64" and "win-64".

• Bug Fixes

• Clarified the checkout process for the publishing jobs in the CI-CD workflow.

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Detailed Changes: v1.25.0...v1.26.0

v1.25.0

v1.25.0 (2024-12-16)

Features

• Add optional segmentationLabel input for singleRadiomifFetaureExtraction (#90, bebb8f3)

Discovered an edge case when processing ISPY2 SEG files that have multiple regions in them that are identified by numeric values in the mask.

Need READII to be able to take a specific value so the correct mask is used when checking the mask, cropping the image, and performing feature extraction.

## Summary by CodeRabbit

• New Features - Introduced an optional segmentationLabel parameter in the feature extraction process for enhanced flexibility. - Improved error handling during segmentation mask validation and image cropping.

• Bug Fixes - Enhanced robustness by catching and logging exceptions related to feature extraction.

• Tests - Added new tests to verify behavior with the segmentationLabel parameter and to validate error handling for invalid inputs.

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Detailed Changes: v1.24.0...v1.25.0

v1.24.0

v1.24.0 (2024-12-16)

Features

• Add data functions used for analysis code (#89, 2eb6e1e)

Summary by CodeRabbit

• New Features

• Introduced functions for manipulating and analyzing patient data, including patient ID handling and time conversion.

• Added capabilities for selecting and filtering radiomic data within DataFrames.

• Implemented methods for replacing values and splitting DataFrames based on specified criteria.

• Bug Fixes

• Enhanced error handling across multiple functions to ensure robust performance and logging of issues.

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Detailed Changes: v1.23.0...v1.24.0

v1.23.0

v1.23.0 (2024-12-13)

Features

• Add io/loaders module (#83, 81fbd78)

Includes features, general, and images specific loading functions

• New Features
• Introduced a new module for loading various data types in the READII pipeline.
• Added functions for loading imaging feature sets, dataset configurations, and data files into DataFrames.

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Detailed Changes: v1.22.0...v1.23.0

v1.22.0

v1.22.0 (2024-12-13)

Features

• Add BaseWriter, and example NIFTIWriter with notebooks documenting them (#84, 7228770)

Mostly inspired and reusing logic from Med-ImageTools DICOMSorter design

• New Features
• Enhanced Jupyter notebooks for saving medical imaging data in NIFTI format and CSV metadata.
• Added examples for using subclasses of BaseWriter for writing text and CSV files.
• Introduced the NIFTIWriter class for managing NIFTI file writing with validation and error handling.
  • Added new CSVWriter class for saving data in CSV format.

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Detailed Changes: v1.21.0...v1.22.0

v1.21.0

v1.21.0 (2024-12-13)

Features

• Add readii-datasets CLI command and include orcestra-downloader dependency (#80, f760b68)

closes bhklab/analyze_readii_outputs#6

the CLI in orcestra-downloader uses click and allows us to reuse the same user CLI API for just a subset of the data and so the readii-datasets entry point is just a renamed version of that one to prevent rewriting code.

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Detailed Changes: v1.20.0...v1.21.0

v1.20.0

v1.20.0 (2024-12-12)

Features

• Initialize documentation (#85, 3b2c294)

Start of documentation, mostly copied the core dependencies and plugins from med-imagetools

• Set up initial documentation structure using MkDocs, including configuration and integration of Markdown files for the README and CHANGELOG.

this "core" would be the base of the main vs 2.0 branch

## Summary by CodeRabbit

• New Features - Added badges for project health and status in the README. - Expanded installation instructions with a new environment setup method. - Introduced a section for serving documentation locally.

• Documentation - Enhanced clarity and structure of the README, including command-line options and contributing guidelines. - Updated inclusion method for CHANGELOG and README in documentation. - Introduced a new configuration file for MkDocs documentation, improving navigation and usability.

• Bug Fixes - Corrected formatting for bash commands in the README to enhance readability.

• Chores - Updated project version and dependencies in the configuration files.

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Detailed Changes: v1.19.0...v1.20.0

v1.19.0

v1.19.0 (2024-12-11)

Features

• Add abstract and concrete classes for negative controls and regions (#81, c10a568)

4D-Lung

Order of operations

1. negative_control_strategy(image, mask=mask, region=region_strategy) 2. runs the __call__ on the negative_control_strategy 3. which runs the __call__ of region(image_array, mask_array) 4. the result of which is used to figure out what indices of the original image to apply the transform method of the NegativeControlStrategy concrete classes to 5. only replace the region indices image_array[mask_indices] = transformed_values

Resource on Strategy Pattern: https://refactoring.guru/design-patterns/strategy/python/example

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Co-authored-by: Katy Scott [email protected]

Refactoring

• Update Ruff configuration and refactor codebase (#68, e88e704)

Enhance the Ruff configuration to include additional files and ignore specific PEP-8 naming conventions. Refactor the codebase by replacing os.path with pathlib, improving logging verbosity, adding type annotations, and organizing imports.

• Bug Fixes

• Improved error handling for image cropping and feature extraction processes, ensuring robustness and clearer logging.

• Chores

• Updated configuration settings to refine linting rules and file inclusions, optimizing code quality checks.

• Incremented Pixi version across CI-CD jobs for improved performance.

• feature-extraction: Extract-method refactor to simplify workflow, prepare for class-based feature extraction (#69, 3bcaa28)

summary: Refactor code to improve readability, logging, and type annotations while addressing various bugs and updating dependencies.

mostly extract-method refactoring to make following code flow a bit easier. - setting up to create a class for the module to save from passing around all the parameters

updates to code quality control tasks - for the most part will follow suit with med-imagetools configuration for qc - pixi run qc will run ruff format and lint on files included in ruff.toml - Enhance ruff configuration to include additional files and ignore specific PEP-8 naming conventions.

• New Features - Introduced new functions for enhanced radiomic feature extraction: generateNegativeControl, cropImageAndMask, and featureExtraction.

• Improvements - Enhanced error handling and logging for the feature extraction process. - Improved documentation and formatting in loaders for better readability.

• Configuration Updates - Updated linting configuration to include specific files for checks and clarified linting rules with detailed comments. - Updated project version to "1.18.0" and added new dependencies for Jupyter-related packages. - Streamlined CI-CD workflow by modifying linting commands and removing unnecessary jobs.

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Detailed Changes: v1.18.0...v1.19.0